A Portable Readout System for Biomarker Detection with Aptamer-Modified CMOS ISFET Array.

Biosensors based on ion-sensitive field effect transistors (ISFETs) combined with aptamers offer a promising and convenient solution for point-of-care testing applications due to the ability for fast and label-free detection of a wide range of biomarkers. Mobile and easy-to-use readout devices for the ISFET aptasensors would contribute to further development of the field. In this paper, the development of a portable PC-controlled device for detecting aptamer-target interactions using ISFETs is described. The device assembly allows selective modification of individual ISFETs with different oligonucleotides. Ta2O5-gated ISFET structures were optimized to minimize trapped charge and capacitive attenuation. Integrated CMOS readout circuits with linear transfer function were used to minimize the distortion of the original ISFET signal. An external analog signal digitizer with constant voltage and superimposed high-frequency sine wave reference voltage capabilities was designed to increase sensitivity when reading ISFET signals. The device performance was demonstrated with the aptamer-driven detection of troponin I in both reference voltage setting modes. The sine wave reference voltage measurement method reduced the level of drift over time and enabled a lowering of the minimum detectable analyte concentration. In this mode (constant voltage 2.4 V and 10 kHz 0.1Vp-p), the device allowed the detection of troponin I with a limit of detection of 3.27 ng/mL. Discrimination of acute myocardial infarction was demonstrated with the developed device. The ISFET device provides a platform for the multiplexed detection of different biomarkers in point-of-care testing.

Aptamers Targeting Cardiac Biomarkers as an Analytical Tool for the Diagnostics of Cardiovascular Diseases: A Review.

The detection of cardiac biomarkers is used for diagnostics, prognostics, and the risk assessment of cardiovascular diseases. The analysis of cardiac biomarkers is routinely performed with high-sensitivity immunological assays. Aptamers offer an attractive alternative to antibodies for analytical applications but, to date, are not widely practically implemented in diagnostics and medicinal research. This review summarizes the information on the most common cardiac biomarkers and the current state of aptamer research regarding these biomarkers. Aptamers as an analytical tool are well established for troponin I, troponin T, myoglobin, and C-reactive protein. For the rest of the considered cardiac biomarkers, the isolation of novel aptamers or more detailed characterization of the known aptamers are required. More attention should be addressed to the development of dual-aptamer sandwich detection assays and to the studies of aptamer sensing in alternative biological fluids. The universalization of aptamer-based biomarker detection platforms and the integration of aptamer-based sensing to clinical studies are demanded for the practical implementation of aptamers to routine diagnostics. Nevertheless, the wide usage of aptamers for the diagnostics of cardiovascular diseases is promising for the future, with respect to both point-of-care and laboratory testing.

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

NORWEGIAN-RUSSIAN COOPERATION IN NUCLEAR LEGACY REGULATION: CONTINUING EXPERIENCE AND LESSONS.

Safe management of nuclear legacies arising from past activities is a critical issue in maintaining confidence for the continuing and future use of radioactive materials. Effective and efficient regulatory supervision of nuclear legacy management is a critical part of that process. The Norwegian Radiation Protection Authority plays an active role in bilateral regulatory cooperation projects with sister authorities in the Russian Federation, as part of Norway's Plan of Action to improve radiation and nuclear safety. Based on this experience and by reference to specific legacy sites and facilities, this study provides an overview of the substantial progress made in remediation at the Site of Temporary Storage for spent fuel and radioactive waste at Andreeva Bay and presents radiation protection issues arising from the experience and lessons learned in this work. It is suggested that this experience can be useful in the further development of international recommendations, standards and guidance on remediation of nuclear legacies.

Discovering chemistry with an ab initio nanoreactor.

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

Generating Efficient Quantum Chemistry Codes for Novel Architectures.

We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures.

Peculiarities of the complexation of copper and silver adducts of a 3,5-bis(trifluoromethyl)pyrazolate ligand with organoiron compounds.

Interaction of the copper, {[3,5-(CF(3))(2)Pz]Cu}(3), and silver, {[3,5-(CF(3))(2)Pz]Ag}(3), macrocycles [3,5-(CF(3))(2)Pz = 3,5-bis(trifluoromethyl)pyrazolate] with cyclooctatetraeneiron tricarbonyl, (cot)Fe(CO)(3), was investigated by IR and NMR spectroscopy for the first time. The formation of 1:1 complexes was observed at low temperatures in hexane. The composition of the complexes (1:1) and their thermodynamic characteristics in hexane and dichloromethane were determined. The π-electron system of (cot)Fe(CO)(3) was proven to be the sole site of coordination in solution and in the solid state. However, according to the single-crystal X-ray data, the complex has a different (2:1) composition featuring the sandwich structure. The complexes of ferrocene with copper and silver macrocycles have a columnar structure (X-ray data).

Sandwiched graphene--membrane superstructures.

We demonstrate by molecular dynamics simulations that graphene sheets could be hosted in the hydrophobic interior of biological membranes formed by amphiphilic phospholipid molecules. Our simulation shows that these hybrid graphene--membrane superstructures might be prepared by forming hydrated micelles of individual graphene flakes covered by phospholipids, which can be then fused with the membrane. Since the phospholipid layers of the membrane electrically isolate the embedded graphene from the external solution, the composite system might be used in the development of biosensors and bioelectronic materials.

Controllable synthetic molecular channels: biomimetic ammonia switch.

We use molecular dynamics simulations combined with iterative screening to test if one can design mechanically controllable and selective molecular pores. The first model pore is formed by two stacked carbon nanocones connected by aliphatic chains at their open tips, in analogy to aquaporins. It turns out that when one nanocone is gradually rotated with respect to the other, the molecular chains alter the size of the nanopore formed at the cone tips and control the flow rates of liquid pentane through it. The second model pore is formed by two carbon nanotubes joined by a cylindrical structure of antiparallel peptides. By application of a torque to one of the nanotubes, while holding the other, we can reversibly fold the peptides into forward or backward-twisted barrels. We have modified the internal residues in these barrels to make these pores selective and controllable. Eventually, we found a nanopore that in the two folded configurations has very different transmission rates for hydrated NH(3) molecules.

Modeling the self-assembly of colloidal nanorod superlattices.

We model the self-assembly of superlattices of colloidal semiconducting nanorods horizontally and vertically oriented on material substrates. The models include van der Waals and Coulombic coupling between nanorods with intrinsic electric dipoles and their coupling to the substrates. We also investigate the effect of external electric fields on the self-assembly processes. Our theoretical predictions for stable self-assembled superlattices agree well with the available experimental data.

Dipole-dipole interactions in nanoparticle superlattices.

Nanoparticles often self-assemble into hexagonal-close-packed (hcp) structures although it is predicted to be less stable than face-centered-cubic (fcc) packing in hard-sphere models. In addition to close-packed fcc and hcp superlattices, we observe formation of nonclose-packed simple-hexagonal (sh) superlattices of nearly spherical PbS, PbSe, and gamma-Fe2O3 nanocrystals. This surprisingly rich phase diagram of monodisperse semiconducting nanoparticles is explained by considering the interactions between nonlocal dipoles of individual nanoparticles. By calculating the total electrostatic and dispersive energies, we explain stability of the hcp and sh nanoparticle superlattices, introduce the superlattice phase diagram, and predict antiferroelectric ordering in dipolar nanoparticle superlattices.